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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs10371          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:52/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NM_130767.1:c.1207G>A
NM_130767.2:c.1207G>A
NP_570123.1:p.Ala403Thr
NT_006713.14:g.31226000C>T
Links , Linkout

SNP Details are organized in the following sections:
Submission Fasta Resource GeneView Map Diversity Validation

  Submitter records for this RefSNP Cluster back to top
The submission ss17069119 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs10371 during BLAST analysis for the current build.

NCBI
Assay ID		Handle|Submitter IDValidation
Status		ss to rs
Orientation
/Strand		Alleles5' Near Seq 30 bp3' Near Seq 30 bpEntry
Date		Update
Date		Build
Added		Molecule
Type		Freq
Warning		Ancestral
Allele		Success
Rate
ss12523CGAP-GAI|55557byFreqfwd/BC/Tgctttgtaaagtcagacaagagacgataagcaaatgtgctggacttcccacgtgcttttc08/23/9904/07/0452cDNA99 %
ss1530425LEE|533689rev/TA/Ggaaaagcacgtgggaagtccagcacatttgcttatcgtctcttgtctgactttacaaagc09/13/0010/25/06103cDNAunknown
ss4419843LEE|e533689rev/TA/Ggaaaagcacgtgggaagtccagcacatttgcttatcgtctcttgtctgactttacaaagc04/26/0210/10/03106cDNAunknown
ss17069119CSHL-HAPMAP|CSHL-HuAA-200402.chr5.NT_006713.13_10023774byFreqfwd/BC/Tgctttgtaaagtcagacaagagacgataagcaaatgtgctggacttcccacgtgcttttc02/17/0405/16/04120Genomicunknown
ss48428486APPLERA_GI|hCV7439646byFreqfwd/BC/Tgctttgtaaagtcagacaagagacgataagcaaatgtgctggacttcccacgtgcttttc09/28/0511/03/06126Genomicunknown
ss66632407ILLUMINA|HumanHap300v1.1_rs10371fwd/BC/Tgctttgtaaagtcagacaagagacgataagcaaatgtgctggacttcccacgtgcttttc11/09/0611/09/06127Genomicunknown
ss66881344ILLUMINA|HumanHap550v1.1_rs10371fwd/BC/Tgctttgtaaagtcagacaagagacgataagcaaatgtgctggacttcccacgtgcttttc11/14/0611/14/06127Genomicunknown
ss66972777ILLUMINA|HumanHap650Yv1.0_rs10371fwd/BC/Tgctttgtaaagtcagacaagagacgataagcaaatgtgctggacttcccacgtgcttttc11/14/0611/14/06127Genomicunknown
ss68940385PERLEGEN|PGP04050326byFreqfwd/BC/Tgctttgtaaagtcagacaagagacgataagcaaatgtgctggacttcccacgtgcttttc01/30/0708/14/07127Genomicunknown
ss70364713ILLUMINA|HumanHap300v2.0_rs10371fwd/BC/Tgctttgtaaagtcagacaagagacgataagcaaatgtgctggacttcccacgtgcttttc04/18/0711/17/07127Genomicunknown
ss70477045ILLUMINA|HumanHap550v3.0__rs10371rev/TA/Ggaaaagcacgtgggaagtccagcacatttgcttatcgtctcttgtctgactttacaaagc04/20/0703/29/08130Genomicunknown
ss71000068ILLUMINA|HumanHap650Yv3.0_rs10371fwd/BC/Tgctttgtaaagtcagacaagagacgataagcaaatgtgctggacttcccacgtgcttttc04/23/0704/23/07127Genomicunknown
ss74808997AFFY|SNP_M-181552fwd/BC/Tgctttgtaaagtcagacaagagacgataagcaaatgtgctggacttcccacgtgcttttc08/09/0708/09/07128Genomicunknown
ss75686073ILLUMINA|ILMN_Human_1M_rs10371fwd/BC/Tgctttgtaaagtcagacaagagacgataagcaaatgtgctggacttcccacgtgcttttc08/28/0708/29/07129Genomicunknown
ss76827973AFFY|AFFY_6_1M_SNP_A-8689637fwd/BC/Tgacaagagacgataagcaaatgtgctggactt08/28/0708/30/07129Genomicunknown
ss78139248HGSV|Cor12878_SNV_20070510.chr5_80667398fwd/BC/Tgctttgtaaagtcagacaagagacgataagcaaatgtgctggacttcccacgtgcttttc10/17/0710/18/07129Genomicunknown
ss83349515KRIBB_YJKIM|KHS440639fwd/BC/Tgctttgtaaagtcagacaagagacgataagcaaatgtgctggacttcccacgtgcttttc12/04/0712/04/07130Genomicunknown
ss84734862HGSV|Cor18517_SNV_20070510.chr5_80667398fwd/BC/Tgctttgtaaagtcagacaagagacgataagcaaatgtgctggacttcccacgtgcttttc12/06/0712/07/07130Genomicunknown
ss1091656931000GENOMES|CEU.trio.12.15.2008_1297121_chr5_80667398fwd/BC/Tgctttgtaaagtcagacaagagacgataagcaaatgtgctggacttcccacgtgcttttc12/15/0812/16/08130Genomicunknown
ss116686956ILLUMINA-UK|NA18507_000100899_NCBI36.1_chr5_80667398fwd/BC/Tgctttgtaaagtcagacaagagacgataagcaaatgtgctggacttcccacgtgcttttc01/17/0901/17/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs10371|allelePos=468|totalLen=668|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 AGATCAAACt ttatttttat tttaattttt gacagggtct cctgtgtcac ccaggctaga
 gtgcagtggt gtgatcttgg ctcactgtag ccttgacctc ccagactcat gcaatcctcc
 cacctgggtc tcccgggtag ctaggattac aggcatgcac caccatgtcc agctaatttt
 tgtgtatttt atagagatgg gctttcacca tgttgcccag gctggtcttg aactcccgga
 ctcaactatc cacctgcctc agcctcccaa agtgctATGC TGGGTCAAAC TTCTAAAAAT
 ACTCTTTAAA CAATGGGTCA CACATTGGAC GATGGAGATG GACTTCAGTA TGGAGATCAT
 CTTTTACATT ATGTCAAGGT TGATTGAGAA AAATTTTTAA ATTTGTTCTT ACACAAAATG
 GGGGTCCCAC AAAGGTCGCT TTGTAAAGTC AGACAAGAGA CGATAAG
 Y
 CAAATGTGCT GGACTTCCCA CGTGCTTTTC AACCCAAACA GATAAAACAT CATGCTCTTC
 CAGAGTATAT ATTTTTATCT AAAAGACAAC AAAAAAATTA AATTACGAAA GAAAACTGAT
 GCTTTTACTT TAGAAACCAT ATGCATATAT ATGTAGTCAT AGACCAATTG CACTAACTAA
 GGCATCTTAT TTCCTGGATG

  GeneView back to top

GeneView via analysis of contig annotation:  

View more variation on this gene (click to hide).
Include clinically associated: in gene region cSNP has frequency double hit
Assembly SNP to Chr Chr Chr position Contig Contig position Allele
Function mRNA Protein
mRNA to Chr Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

GeneView via analysis of contig annotation: N/A.

GeneView via direct blast against RefSeq sequences (used when no gene model is available):

Function Chr mRNA Protein
SNP to mRNA Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A


  Integrated Maps: back to top
Genome Build Chr Chr Pos Contig Contig Pos SNP to
Chr		 Contig
allele		 Group term Group label Contig label Neighbor
SNP		 Map Method
doesn't map to any assembly.

  NCBI Resource Links back to top
Resource
Submitter-Referenced
GenBank
NT_006713 Hs.108311 W88442
dbSNP Blast Analysis
UniGene Cluster ID
439127

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/C
 C/T
 T/T
 HWP C
 T
ss12523 POOLED_CEPH 188 AF 0.197 0.803
ss17069119 CEPH 184 AF 0.800 0.200
HapMap-CEU European 120 IG 0.667 0.250 0.083 0.100 0.792 0.208
HapMap-HCB Asian 88 IG 0.977 0.023 1.000 0.989 0.011
HapMap-JPT Asian 88 IG 1.000 1.000
HapMap-YRI Sub-Saharan African 120 IG 0.700 0.283 0.017 0.655 0.842 0.158
ss48428486 AGI_ASP population multiple 60 IG 0.700 0.267 0.033 1.000 0.833 0.167
ss68940385 HapMap-CEU European 120 GF 0.667 0.250 0.083 0.792 0.208
HapMap-HCB Asian 90 GF 0.978 0.022 0.989 0.011
HapMap-JPT Asian 90 GF 1.000 1.000
HapMap-YRI Sub-Saharan African 120 GF 0.700 0.283 0.017 0.842 0.158
Concordant Genotype Total Sample C/C C/T T/T
ss17069119 1129 828 254 24
ss48428486 34 21 8 1
ss68940385 269 207 55 7
RefSNP Genotype Summary Total Individual C/C C/T T/T
rs10371 1164 866 269 25
Discordant Genotypes:
Indiviudal
SampleID		 SubSNP(ss) Genotype Population
Handle		 Submitter
Population		 Submitter
SampleID		 SampleID
Alias		 Submission
Batch		 NCBI
ProbeID
5242 ss17069119 T/T CSHL-HAPMAP HapMap-YRI NA18508 YOR009.02 r27_ch5_YRI_illumina:human_1m_beadchip 488422
5242 ss68940385 T/T CSHL-HAPMAP HapMap-YRI NA18508 YOR009.02 chr5-HapMap-YRI
Genotype data submitted for1164 samples from1164 individualsIndividual with multiple genotypes submission:270

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqbySubmitterwithHapMapFreqWith1000GenomeData
Validated by: ILLUMINA
 UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .